X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fmath%2FMatrix.java;h=ad914646549386777670575772c86b2b85f5604b;hb=refs%2Fheads%2Ffeature%2FJAL-4307_hetatm_showhide;hp=b910a7edb4229221c06ea32549489d604b3fcb63;hpb=11ec9d4540710b65b82b8b901de07b441c130887;p=jalview.git

diff --git a/src/jalview/math/Matrix.java b/src/jalview/math/Matrix.java
index b910a7e..ad91464 100755
--- a/src/jalview/math/Matrix.java
+++ b/src/jalview/math/Matrix.java
@@ -24,6 +24,7 @@ import jalview.util.Format;
 import jalview.util.MessageManager;
 
 import java.io.PrintStream;
+import java.util.Arrays;
 
 /**
  * A class to model rectangular matrices of double values and operations on them
@@ -215,7 +216,17 @@ public class Matrix implements MatrixI
       System.arraycopy(value[i], 0, newmat[i], 0, value[i].length);
     }
 
-    return new Matrix(newmat);
+    Matrix m = new Matrix(newmat);
+    if (this.d != null)
+    {
+      m.d = Arrays.copyOf(this.d, this.d.length);
+    }
+    if (this.e != null)
+    {
+      m.e = Arrays.copyOf(this.e, this.e.length);
+    }
+
+    return m;
   }
 
   /**
@@ -453,7 +464,7 @@ public class Matrix implements MatrixI
           }
           else
           {
-            // System.out.println("Iteration " + iter);
+            // jalview.bin.Console.outPrintln("Iteration " + iter);
           }
 
           g = (d[l] - d[l - 1]) / (2.0 * e[l - 1]);
@@ -717,7 +728,7 @@ public class Matrix implements MatrixI
           }
           else
           {
-            // System.out.println("Iteration " + iter);
+            // jalview.bin.Console.outPrintln("Iteration " + iter);
           }
 
           g = (d[l] - d[l - 1]) / (2.0 * e[l - 1]);
@@ -961,4 +972,54 @@ public class Matrix implements MatrixI
       }
     }
   }
+
+  @Override
+  public void setD(double[] v)
+  {
+    d = v;
+  }
+
+  @Override
+  public void setE(double[] v)
+  {
+    e = v;
+  }
+
+  public double getTotal()
+  {
+    double d = 0d;
+    for (int i = 0; i < this.height(); i++)
+    {
+      for (int j = 0; j < this.width(); j++)
+      {
+        d += value[i][j];
+      }
+    }
+    return d;
+  }
+
+  /**
+   * {@inheritDoc}
+   */
+  @Override
+  public boolean equals(MatrixI m2, double delta)
+  {
+    if (m2 == null || this.height() != m2.height()
+            || this.width() != m2.width())
+    {
+      return false;
+    }
+    for (int i = 0; i < this.height(); i++)
+    {
+      for (int j = 0; j < this.width(); j++)
+      {
+        double diff = this.getValue(i, j) - m2.getValue(i, j);
+        if (Math.abs(diff) > delta)
+        {
+          return false;
+        }
+      }
+    }
+    return true;
+  }
 }